Next generation DNA sequencing of pediatric AML patient tumors

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Brian Wilhelm, PhD

Brian Wilhelm completed his PhD with Dr. Dixie Mager at the Terry Fox Lab (BC Cancer Research Center) in Vancouver studying transcriptional regulation of a family of immune receptor genes. In order to pursue more global studies of this topic, he then took a post-doctoral position in Dr. Jurg Bahler’s microarray lab at the Wellcome Trust Sanger Institute (Cambridge, UK), where he used fission yeast as a model organism. While there, he led a study to map all transcribed regions in the S. pombe genome, at basepair resolution, using next-generation DNA sequencing (NGS) technology. Upon returning to Canada, he continued his post-doctoral training in the lab of Dr. Guy Sauvageau at the IRIC, before starting his own independent lab investigating the genetic changes that occur in acute myeloid leukemia. Given his research interest in transcriptional regulation, and especially deregulation in the context of cancer, the opportunity to pursue research characterizing AML using high throughput techniques is ideally suited to his background.

In 2009, approximately 4500 Canadians will be diagnosed with leukemia. Despite ongoing research efforts and improvements in treatment approaches, the molecular mechanisms that cause normal karyotype acute myeloid leukemia (AML-NK) are poorly understood and patients with leukemia have the one of lowest survival rates of any form of cancer, with only twenty percent surviving past 5 years. Nearly a third of all patients with leukemia will develop acute myeloid leukemia (AML) and half of these patients will have a normal chromosomal karyotype (AML-NK). The lack of cytogenetic information as to the causes of this disease represents a major obstacle in the diagnosis and guided treatment of these patients. Extensive efforts to find genes recurrently mutated in AML-NK, have identified only a few so far, (e.g. nucleophosmin 1 (NPM1), FMS-like tyrosine kinase 3 (FLT3), DNA (cytosine-5)-methyltransferase 3A (DNMT3A),CCAAT/enhancer binding protein alpha (CEBPα)) however even these mutations are not universally present in AML patients. This strongly suggests that there are additional uncharacterized molecular lesions which are required for the development of AML-NK that could represent novel therapeutic targets.

In order to identify genetic changes associated with the development of NK-AML, Brian will be using next generation DNA sequencing technology of AML patient tumors. He is currently involved in a collaborative project using this approach to study adult NK-AML in order to comprehensively identify the genes which have a causative role in the development of AML-NK using samples previously collected and cytogenetically characterized at the Banque de Cellules Leucémiques du Québec (BCLQ). The ability to sequence the equivalent of entire human genomes from leukemic RNA (RNA-seq) will allow him to identify any putative mutations in patient samples with basepair resolution. In addition, Brian will apply these same cutting edge approaches to characterize paediatric AML samples, in order to understand the possible role of inherited genetic predisposition for the development of AML in children. Together, these data will provide an unprecedented amount of information regarding the genes mutated in NK-AML, an essential precursor to allow the eventually development of novel targeted therapies.